Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004241.1 Hibiscus syriacus cultivar Beakdansim tig00009299_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 59288
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:545 original size:21 final size:21
Alignment explanation
Indices: 521--560 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
511 CAGATTGCTC
521 AGAGGGAACCGATTCCCCCGA
1 AGAGGGAACCGATTCCCCCGA
*
542 AGAGGGTACCGATTCCCCC
1 AGAGGGAACCGATTCCCCC
561 TGAATGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.28, T:0.12
Consensus pattern (21 bp):
AGAGGGAACCGATTCCCCCGA
Found at i:2662 original size:23 final size:23
Alignment explanation
Indices: 2618--2662 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2608 TGATGATCTT
* * * *
2618 AAAACTTTTTGATAAGTTGGAAC
1 AAAACGTTTTGAAAAATGGGAAC
2641 AAAACGTTTTGAAAAATGGGAA
1 AAAACGTTTTGAAAAATGGGAA
2663 AATTCAAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (23 bp):
AAAACGTTTTGAAAAATGGGAAC
Found at i:6293 original size:23 final size:22
Alignment explanation
Indices: 6251--6334 Score: 98
Period size: 22 Copynumber: 3.8 Consensus size: 22
6241 TTAGTACAGA
*
6251 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
6273 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
6296 GGGAACCGATTCCCTCC-TGTAG
1 GGGAACCGATACCC-CCTTGAAG
*
6318 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
6335 GAGGTTCTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
21 2 0.04
22 30 0.56
23 20 0.37
24 2 0.04
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:7923 original size:18 final size:18
Alignment explanation
Indices: 7888--7926 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
7878 AGAGCAACAC
* *
7888 GAGGAACAAGCACCTCCA
1 GAGGAACAACCACATCCA
*
7906 GAGGAACAACCTCATCCA
1 GAGGAACAACCACATCCA
7924 GAG
1 GAG
7927 TATCAAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.23, T:0.08
Consensus pattern (18 bp):
GAGGAACAACCACATCCA
Found at i:12669 original size:27 final size:28
Alignment explanation
Indices: 12614--12675 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
12604 TAAAACATCT
* * *
12614 ACTTGTATAAAATAGTAAGTTATTTAAA
1 ACTTTTATAAAATAGTAACTTATTCAAA
*
12642 ACTTTTATAACATA-TAACTTATTCAAA
1 ACTTTTATAAAATAGTAACTTATTCAAA
*
12669 ACGTTTA
1 ACTTTTA
12676 CAGAACTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (28 bp):
ACTTTTATAAAATAGTAACTTATTCAAA
Found at i:13606 original size:32 final size:32
Alignment explanation
Indices: 13487--13611 Score: 123
Period size: 31 Copynumber: 4.0 Consensus size: 32
13477 AACCTCGACA
* * * * *
13487 ACTGTCCATAGGTCCCGAAGAACCTAAGTAA-
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
**
13518 ACTGTCCATATGTTCTTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
*
13549 ACTGTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
*
13581 TCTGTCCATATGTTCCGTAGAACATAGGTAA
1 ACTGTCCATATGTTCCGTAGAACATAGGTAA
13612 ACCCTCGACT
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
30 5 0.07
31 42 0.55
32 25 0.33
33 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:14019 original size:25 final size:24
Alignment explanation
Indices: 13965--14019 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
13955 AGTCACATTT
*
13965 CATATAACACTTATATTACATATT
1 CATATAACACTTATATTACATATA
* *
13989 CTTATAATTACTTATATTA-ATATCA
1 CATATAA-CACTTATATTACATAT-A
14014 CATATA
1 CATATA
14020 TCACAAGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (24 bp):
CATATAACACTTATATTACATATA
Found at i:15778 original size:72 final size:72
Alignment explanation
Indices: 15654--15793 Score: 208
Period size: 72 Copynumber: 1.9 Consensus size: 72
15644 TTTCTAAAAT
* * * *
15654 GTGATATATGCACATGCATATGAACAATCCTTATTCTCAGAATTTGCACCCTAATGATTATATAT
1 GTGACATATGCACATGCATATCAACAATCCTTACTCTCAGAATTTGCACCCTAATGATTATACAT
15719 ATATAAC
66 ATATAAC
* * * *
15726 GTGACATATGCACCTGCATATCAACAATCCTTACTCTCATAATTTGCTCCCTAATGATTTTACAT
1 GTGACATATGCACATGCATATCAACAATCCTTACTCTCAGAATTTGCACCCTAATGATTATACAT
15791 ATA
66 ATA
15794 GAAGATGGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (72 bp):
GTGACATATGCACATGCATATCAACAATCCTTACTCTCAGAATTTGCACCCTAATGATTATACAT
ATATAAC
Found at i:16195 original size:30 final size:31
Alignment explanation
Indices: 16159--16218 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
16149 TTATTTTTAT
*
16159 TTTACCCCTTATT-TTCTATGG-TAATTATAC
1 TTTACCCCTCATTATT-TATGGTTAATTATAC
*
16189 TTTACCCGTCATTATTTATGGTTAATTATA
1 TTTACCCCTCATTATTTATGGTTAATTATA
16219 TTTTGCTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (31 bp):
TTTACCCCTCATTATTTATGGTTAATTATAC
Found at i:19481 original size:13 final size:13
Alignment explanation
Indices: 19443--19484 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
19433 ACCGGTCACT
*
19443 ACCCGACCCGTTT
1 ACCCGACCCGTTG
19456 ACCCGACCCGTTG
1 ACCCGACCCGTTG
19469 ACCCGACCCGTTG
1 ACCCGACCCGTTG
19482 ACC
1 ACC
19485 GTTGACCGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.17, C:0.48, G:0.19, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:20806 original size:18 final size:18
Alignment explanation
Indices: 20780--20814 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20770 TCGAAAGGAC
*
20780 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
20798 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
20815 CCGGATGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:25950 original size:23 final size:23
Alignment explanation
Indices: 25913--25956 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
25903 TCTGAATGAT
*
25913 ACAGTGCTGACTGATTCAACAAA
1 ACAGTGCTGAATGATTCAACAAA
*
25936 ACAGTGTTGAATGATTCAACA
1 ACAGTGCTGAATGATTCAACA
25957 CAGAAATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (23 bp):
ACAGTGCTGAATGATTCAACAAA
Found at i:26739 original size:23 final size:24
Alignment explanation
Indices: 26700--26745 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
26690 AAATATTATT
*
26700 TAATATTTAAAATATATTTATAAA
1 TAATATTTAAAATATATTAATAAA
26724 TAAT-TTTAATAA-ATATTAATAA
1 TAATATTTAA-AATATATTAATAA
26746 TTACTTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATATTTAAAATATATTAATAAA
Found at i:31887 original size:16 final size:16
Alignment explanation
Indices: 31866--31897 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31856 AATAAATAAG
31866 CGAACATAAACGAACA
1 CGAACATAAACGAACA
31882 CGAACATAAACGAACA
1 CGAACATAAACGAACA
31898 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:31985 original size:16 final size:16
Alignment explanation
Indices: 31964--32010 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
31954 TTTAATAAAT
31964 ACACGAACATAAACGA
1 ACACGAACATAAACGA
*
31980 ACACGAACATAAATGA
1 ACACGAACATAAACGA
31996 ACACGAACATAAACG
1 ACACGAACATAAACG
32011 TTAGAGACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.09
Consensus pattern (16 bp):
ACACGAACATAAACGA
Found at i:35905 original size:24 final size:24
Alignment explanation
Indices: 35870--35931 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
35860 TATTATGTTA
*
35870 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
*
35894 AACATAACTGAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
35918 AACATAACCGAACG
1 AACATAACTGAACG
35932 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.52, C:0.23, G:0.13, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:35952 original size:34 final size:34
Alignment explanation
Indices: 35874--35954 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 34
35864 ATGTTAAACA
*
35874 TAAATGAACGCACATAAACGAACATAACTGAACG
1 TAAATGAACGAACATAAACGAACATAACTGAACG
* * * * * *
35908 CATATAAACGAACATAACCGAACGTTCAC-GAACG
1 TAAATGAACGAACATAAACGAAC-ATAACTGAACG
35942 TAAATGAACGAAC
1 TAAATGAACGAAC
35955 GAGACCTATG
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
34 33 0.92
35 3 0.08
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (34 bp):
TAAATGAACGAACATAAACGAACATAACTGAACG
Found at i:41950 original size:21 final size:21
Alignment explanation
Indices: 41924--41972 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
41914 ACCTAATATT
41924 ACAATGTCAAAATTAGGTGCA
1 ACAATGTCAAAATTAGGTGCA
41945 ACAATGTCAAAATTAGGTGCA
1 ACAATGTCAAAATTAGGTGCA
*
41966 ATAATGT
1 ACAATGT
41973 TTGAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (21 bp):
ACAATGTCAAAATTAGGTGCA
Found at i:50275 original size:20 final size:22
Alignment explanation
Indices: 50235--50277 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
50225 TTTCATTACA
50235 TTTTTATAATTAAATTTTTAAAT
1 TTTTTATAATT-AATTTTTAAAT
50258 TTTTTATAATT-A-TTTTAAAT
1 TTTTTATAATTAATTTTTAAAT
50278 ATAAAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
23 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTATAATTAATTTTTAAAT
Found at i:53513 original size:3 final size:3
Alignment explanation
Indices: 53505--53531 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53495 AATGACATCA
53505 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
53532 TTTTATTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54356 original size:2 final size:2
Alignment explanation
Indices: 54314--54339 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54304 ACATACATAC
54314 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
54340 CAAAGTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56001 original size:2 final size:2
Alignment explanation
Indices: 55994--56028 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
55984 ATTCAATTTA
55994 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56029 GAAGTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57975 original size:19 final size:21
Alignment explanation
Indices: 57928--57973 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
57918 ATAACATTAC
*
57928 AAATCTTACGTACAAATGATA
1 AAATATTACGTACAAATGATA
* *
57949 AAATATTACGTACACATGAAA
1 AAATATTACGTACAAATGATA
57970 AAAT
1 AAAT
57974 TATAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (21 bp):
AAATATTACGTACAAATGATA
Done.